Gap4 stores the data for each sequencing project (e.g. the data for a single cosmid or BAC) in a gap4 assembly database, so at the start of a sequencing project the user should employ gap4 to create the database for the project (see section Opening a New Database). New database are created with sufficient index space for around 8000 readings, but this can be extended if required.
Gel reading data in experiment file format (see section Experiment File Format) is entered into the database using the methods available from the assembly menu (see section Entering Readings into the Database (Assembly)).
To assemble more data for the project or to edit or analyse readings already entered the user should open the same project database (see section Opening an Existing Database).
Although the database files are designed to be free of corruption it is advisable to make regular backups (see section Making Backups of Databases).
Database names can have from one to 240 letters and must not include a full stop or spaces. The database itself consists of two files; a file of records and an index file. If the database is called `FRED' then version 0 of the database comprises the pair of files named `FRED.0' and `FRED.0.aux', the latter of these being the index file. The "version" is the character after the full stop in these filenames. Versions are not limited to numbers alone, but must be single characters.
When a database is opened for writing a `BUSY' file is created. For the
`FRED' database this will be named `FRED.0.BUSY'. When the
database is closed the file is deleted. The file is
used by gap4 to signify that the database is opened for writing and is
part of its mechanism to prevent more than one person editing a
database at any time. Before opening a database for writing,
gap4 checks to see if the BUSY file for that database exists. If it does
the database is opened only for reading, if not it creates the file, so
that any additional attempts to open the database for writing will be
blocked. A side effect of this mechanism, is that
in the event of a program or system crash the BUSY file
will be left on the disk, even though the database is not being used. In
this case users must remove the BUSY file
(after checking that it really isn't in
use!) using, on UNIX the rm command before opening the database. Eg
"rm FRED.0.BUSY". On Windows use the Recycle Bin.
The gap4 database is robustly designed. Killing the program whilst updating the database should never yield an inconsistent state. A "roll-back" mechanism is utilised to undo any partially written updates and revert to the last consistent database. Hence quitting abnormally may result in the loss of some data. Always quit using the Exit command within the File menu.
However it is advised that copies of the database are made regularly to safeguard against any software bugs or disk corruptions.